Chikungunya virus (CHIKV), an NIAID category C priority pathogen, causes incapacitating musculoskeletal disease in humans characterized by an impaired ability to ambulate and intense pain in the peripheral joints that lasts for weeks to months. During the explosive 2004-2007 epidemic of CHIKV that involved millions of patients, infected travelers led directly to the introduction of CHIKV in nonendemic countries. Chikungunya translates as that which bends up the joints, and reflects the debilitating rheumatic symptoms that are experienced by most infected individuals. Up to 64% of patients reported persistent rheumatic symptoms more than one year after initial diagnosis, and 12% still reported symptoms 3-5 years later. Interestingly, chronic joint symptoms associated with CHIKV infection can occur in a cyclic manner, suggesting resurgence of disease symptoms occurs by unknown mechanisms. We have developed a mouse model of CHIKV infection in which the major pathological outcomes, arthritis, myositis, and tenosynovitis, are consistent with the clinical signs experienced by the majority of CHIKV-infected humans. Strikingly, we found that both histopathological changes and CHIKV RNA persisted in joint tissues of CHIKV-inoculated mice for at least three weeks post- inoculation, suggesting that the persistence of virus or viral RNA may drive chronic inflammation. We isolated CHIKV RNA from murine joint tissues at 3 weeks post-inoculation and showed that it was infectious when transfected into cells, indicating that infectious CHIKV genomes persisted in tissues. Based on these studies, we hypothesize that persistence of CHIKV-induced rheumatic disease is associated with persistent CHIKV infection. To test this hypothesis, in Aim 1 we will define the duration and the nature of CHIKV infection and histopathological changes in joint tissues. In addition, we will use 454 sequencing to define the viral genotypes present in persistently infected joint tissue to test the hypothesis that CHIKV persistence in joints is associated with the selection of unique viral variants. Our preliminary studies indicate that CHIKV persists in joint tissue yet is efficiently cleared from non-joint tissues. In Aim 2, we will use a panel of mice with genetically-defined deficiencies in components of the adaptive immune response to define the immunological mechanisms responsible for CHIKV clearance from non-joint tissues. In addition, we will define the extent to which immunosuppression after infection is established is associated with a resurgence of CHIKV replication and rheumatic disease signs. These studies directly address an outstanding question in the field of whether persistent CHIKV-induced rheumatic disease signs are associated with persistent infection. Defining this association and the immunological mechanisms that regulate CHIKV clearance and the sites and duration of infection has important treatment and public health implications, including informing therapeutic strategies for the treatment of chronic CHIKV-induced rheumatic disease symptoms and policies regarding blood and tissue donation in regions with CHIKV activity.